Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
Cell. 2023 Dec 21;186(26):5840-5858.e36. doi: 10.1016/j.cell.2023.11.019.
Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.
短串联重复序列（STR）不稳定性导致几种重复扩展疾病的转录沉默。在脆性 X 综合征（FXS）中，CGG STR 的突变长度扩展通过局部 DNA 甲基化抑制 FMR1。在这里，我们在 FXS 患者来源的 iPSC、iPSC 衍生的神经祖细胞、EBV 转化的淋巴母细胞和具有突变长度 CGG 扩展的脑组织中发现了常染色体上的大片段 H3K9me3 结构域和 X 染色体上的 FMR1 结构域。H3K9me3 结构域通过染色体间相互作用连接，并标记 TAD 和环的严重错误折叠。它们包含在 S 期结束时复制的长突触基因、复制应激诱导的双链断裂以及易发生逐步体细胞不稳定性的 STR。将突变长度的 CGG 通过 CRISPR 工程改造为前突变长度可逆转 X 染色体和多个常染色体上的 H3K9me3，重新折叠 TAD，并恢复基因表达。H3K9me3 结构域也可能出现在通过与基因组不稳定性相关的扰动产生的正常长度 iPSC 中，这表明它们在 FXS 之外具有相关性。我们的研究结果揭示了易不稳定的基因座之间的 Mb 级异染色质化和转座相互作用。
